keyword
MENU ▼
Read by QxMD icon Read
search

Bacterial whole genome sequencing

keyword
https://www.readbyqxmd.com/read/28630127/deciphering-function-of-new-gonococcal-vaccine-antigens-using-phenotypic-microarrays
#1
Benjamin I Baarda, Sarah Emerson, Philip J Proteau, Aleksandra E Sikora
The function and extracellular location of cell envelope proteins make them attractive candidates for developing vaccines against bacterial diseases, including challenging, drug-resistant pathogens such as Neisseria gonorrhoeae Proteomics-driven reverse vaccinology delivered multiple gonorrhea vaccine candidates; however, the biological functions of many of them remain to be elucidated. Herein, the functions of six gonorrhea vaccine candidates - NGO2121, NGO1985, NGO2054, NGO2111, NGO1205, and NGO1344 - in cell envelope homeostasis were probed using phenotype microarrays with 1,056 conditions and a ΔbamE mutant (Δngo1780) as a reference of perturbed outer membrane integrity...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28629503/red-pink-pigmented-hymenobacter-coccineus-sp-nov-hymenobacter-lapidarius-sp-nov-and-hymenobacter-glacialis-sp-nov-isolated-from-rocks-in-antarctica
#2
Ivo Sedláček, Stanislava Králová, Kamila Kýrová, Ivana Mašlaňová, Hans-Jürgen Busse, Eva Staňková, Veronika Vrbovská, Miroslav Němec, Miloš Barták, Pavla Holochová, Pavel Švec, Roman Pantůček
Four rod-shaped and Gram-stain-negative bacterial strains, CCM 8647, CCM 8649T, CCM 8643T and CCM 8648T, were isolated from rock samples collected on James Ross Island, Antarctica. Extensive biotyping, fatty acid profiling, chemotaxonomy, 16S rRNA gene sequencing and whole-genome sequencing was applied to isolates to clarify their taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that all four isolates belonged to the genus Hymenobacter. Strains CCM 8649T and CCM 8647 were most closely related to Hymenobacter arizonensis OR362-8T (94...
June 20, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28615687/multi-drug-resistant-klebsiella-pneumoniae-strains-circulating-in-hospital-setting-whole-genome-sequencing-and-bayesian-phylogenetic-analysis-for-outbreak-investigations
#3
Eleonora Cella, Massimo Ciccozzi, Alessandra Lo Presti, Marta Fogolari, Taj Azarian, Mattia Prosperi, Marco Salemi, Michele Equestre, Francesca Antonelli, Alessia Conti, Marina De Cesaris, Silvia Spoto, Raffaele Antonelli Incalzi, Roberto Coppola, Giordano Dicuonzo, Silvia Angeletti
Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28615466/a-pathotyping-multiplex-pcr-for-haemophilus-parasuis-a-tool-for-the-prediction-of-virulence
#4
Kate J Howell, Lucy A Weinert, Sarah E Peters, Jinhong Wang, Juan Hernandez-Garcia, Roy R Chaudhuri, Shi-Lu Luan, Øystein Angen, Virginia Aragon, Susanna M Williamson, Paul R Langford, Andrew N Rycroft, Brendan W Wren, Duncan J Maskell, Alexander W Tucker
Haemophilus parasuis is a diverse bacterial species found in the upper respiratory tract of pigs that can also cause Glässer's disease and pneumonia. A previous pan-genome study of H. parasuis identified 48 genes that were associated with clinical disease. Here we describe the development of a generalised linear model (termed a pathotyping model) to predict the potential virulence of isolates of H. parasuis, based on a subset of 10 genes from the pan-genome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence...
June 14, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28603521/novel-combined-immune-deficiency-and-radiation-sensitivity-blended-phenotype-in-an-adult-with-biallelic-variations-in-zap70-and-rnf168
#5
Ivan K Chinn, Robert P Sanders, Asbjørg Stray-Pedersen, Zeynep H Coban-Akdemir, Vy Hong-Diep Kim, Harjit Dadi, Chaim M Roifman, Troy Quigg, James R Lupski, Jordan S Orange, I Celine Hanson
With the advent of high-throughput genomic sequencing techniques, novel genetic etiologies are being uncovered for previously unexplained Mendelian phenotypes, and the underlying genetic architecture of disease is being unraveled. Although most of these "mendelizing" disease traits represent phenotypes caused by single-gene defects, a percentage of patients have blended phenotypes caused by pathogenic variants in multiple genes. We describe an adult patient with susceptibility to bacterial, herpesviral, and fungal infections...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28600774/multilocus-sequence-typing-mlst-for-cronobacter-spp
#6
Susan Joseph, Stephen Forsythe
MLST is a molecular typing technique that involves the identification and clustering of bacterial isolates based on the partial sequence analysis of multiple housekeeping genes (generally seven) which are distributed across the length of the genome of the organism. The Cronobacter whole genus MLST scheme can be successfully used for an accurate species level identification and classification of this complex genus.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28600759/whole-genome-enrichment-using-rna-probes-and-sequencing-of-chlamydia-trachomatis-directly-from-clinical-samples
#7
Amanda Claire Brown, Mette T Christiansen
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28600685/aquidulcibacter-paucihalophilus-gen-nov-sp-nov-a-novel-member-of-family-caulobacteraceae-isolated-from-cyanobacterial-aggregates-in-a-eutrophic-lake
#8
Haiyuan Cai, Yuan Shi, Yanan Wang, Henglin Cui, Helong Jiang
A bacterial strain, TH1-2(T), was isolated from cyanobacterial aggregates in the eutrophic Lake Taihu, Jiangsu Province, China. Cells were observed to be Gram-negative, slightly curved and rod-shaped. Optimal growth was obtained at pH 7.0 (range 5.5-8.5) and 30 °C (range 20-37 °C) in trypticase soy broth (TSB) without NaCl. Growth was not observed in TSB with 1.0% (w/v) NaCl added. The cells were found to be positive for oxidase and catalase activities. The major fatty acids were identified as 3-hydroxy hexadecanoic acid (C16:0 3-OH), C16:1 ω5c and summed feature 8 (consisting of C18:1 ω6c and cis-11-Octadecenoic acid (C18:1 ω7c)...
June 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28599670/whole-genome-sequencing-of-an-expec-that-caused-fatal-pneumonia-at-a-pig-farm-in-changchun-china
#9
Ling-Cong Kong, Xia Guo, Zi Wang, Yun-Hang Gao, Bo-Yan Jia, Shu-Ming Liu, Hong-Xia Ma
BACKGROUND: In recent years, highly frequent swine respiratory diseases have been caused by extraintestinal pathogenic Escherichia coli (ExPEC) in China. Due to this increase in ExPECs, this bacterial pathogen has become a threat to the development of the Chinese swine industry. To investigate ExPEC pathogenesis, we isolated a strain (named SLPE) from lesioned porcine lungs from Changchun in China, reported the draft genome and performed comparative genomic analyses. RESULTS: Based on the gross post-mortem examination, bacterial isolation, animal regression test and 16S rRNA gene sequence analysis, the pathogenic bacteria was identified as an ExPEC...
June 9, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28596399/whole-genome-sequence-of-coxiella-burnetii-nine-mile-rsa439-phase-ii-clone-4-a-laboratory-workhorse-strain
#10
Jess A Millar, Paul A Beare, Abraham S Moses, Craig A Martens, Robert A Heinzen, Rahul Raghavan
Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid.
June 8, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28590251/a-primer-on-infectious-disease-bacterial-genomics
#11
REVIEW
Tarah Lynch, Aaron Petkau, Natalie Knox, Morag Graham, Gary Van Domselaar
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time...
October 2016: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/28589129/whole-genome-sequence-analysis-of-antimicrobial-resistance-genes-in-streptococcus-uberis-and-streptococcus-dysgalactiae-isolates-from-canadian-dairy-herds
#12
Julián Reyes Vélez, Marguerite Cameron, Juan Carlos Rodríguez-Lecompte, Fangfang Xia, Luke C Heider, Matthew Saab, J Trenton McClure, Javier Sánchez
The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine-cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/28584149/different-resistance-mechanisms-for-cadazolid-and-linezolid-in-c-difficile-found-by-whole-genome-sequencing-analysis
#13
Patrick Caspers, Hans H Locher, Philippe Pfaff, Sarah Diggelmann, Georg Rueedi, Daniel Bur, Daniel Ritz
Cadazolid (CDZ) is a new antibiotic currently in clinical development for the treatment of Clostridium difficile infections. CDZ interferes with the bacterial protein synthesis machinery. The aim of the present study was to identify resistance mechanisms for CDZ and compare to linezolid (LZD) in C. difficile by whole genome sequencing (WGS) of strains generated by invitro passages and of LZD resistant clinical isolates. Clones of C. difficile 630 selected with CDZ during 46 passages had a maximally 4-fold increased CDZ MIC, while the LZD MIC of clones selected with LZD increased up to 16-fold...
June 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28584143/linezolid-dose-that-maximizes-sterilizing-effect-while-minimizing-toxicity-and-resistance-emergence-for-tuberculosis
#14
Shashikant Srivastava, Gesham Magombedze, Thearith Koeuth, Carleton Sherman, Jotam G Pasipanodya, Prithvi Raj, Edward Wakeland, Devyani Deshpande, Tawanda Gumbo
Linezolid has excellent sterilizing effect in tuberculosis patients, but high adverse event rates. The dose that would maximize efficacy and minimize toxicity is unknown. We performed linezolid dose-effect and dose-scheduling studies in the hollow fiber system model of tuberculosis (HFS-TB) for sterilizing effect. HFS-TB units were treated with several doses to mimic human-like linezolid intrapulmonary pharmacokinetics, and repetitively sampled for drug concentration, total bacterial burden, linezolid-resistant subpopulations, and RNA sequencing over 2 months...
June 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28570142/an-efficient-approach-to-explore-and-discriminate-anomalous-regions-in-bacterial-genomes-based-on-maximum-entropy
#15
Gesiele Almeida Barros-Carvalho, Marie-Anne Van Sluys, Fabricio Martins Lopes
Recently, there has been an increase in the number of whole bacterial genomes sequenced, mainly due to the advancing of next-generation sequencing technologies. In face of this, there is a need to provide new analytical alternatives that can follow this advance. Given our current knowledge about the genomic plasticity of bacteria and that those genomic regions can uncover important features about this microorganism, our goal was to develop a fast methodology based on maximum entropy (ME) to guide the researcher to regions that could be prioritized during the analysis...
June 1, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28552099/bacteriology-and-treatment-of-infections-in-the-upper-and-lower-airways-in-patients-with-primary-ciliary-dyskinesia-adressing-the-paranasal-sinuses
#16
Mikkel Christian Alanin
The respiratory tract is lined with motile cilia that transport respiratory mucus. Primary ciliary dyskinesia (PCD) is a chronic genetic disease caused by mutations in genes responsible for ciliary structure and function. Non-functional airway cilia impair the mucociliary clearance (MCC), causing mucostasis, lung infections and destruction, chronic rhinosinusitis (CRS) and hearing impairment. It is of paramount importance to postpone chronic lung infection mainly with Gram-negative bacteria (GNB) in patients with an impaired MCC...
May 2017: Danish Medical Journal
https://www.readbyqxmd.com/read/28550057/prevalence-and-genomic-characterization-of-escherichia-coli-o157-h7-in-cow-calf-herds-throughout-california
#17
Jay N Worley, Kristopher A Flores, Xun Yang, Jennifer A Chase, Guojie Cao, Shuai Tang, Jianghong Meng, Edward R Atwill
Escherichia coli serotype O157:H7 (E. coli O157:H7) is a zoonotic food- and waterborne bacterial pathogen that has a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, like cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle present food safety challenges on a uniquely large scale...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28541480/alternative-evolutionary-paths-to-bacterial-antibiotic-resistance-cause-distinct-collateral-effects
#18
C Barbosa, V Trebosc, C Kemmer, P Rosenstiel, R Beardmore, H Schulenburg, G Jansen
When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To date, the presence and molecular basis of collateral sensitivity has only been studied in few bacterial species and is unknown for opportunistic human pathogens such as Pseudomonas aeruginosa. In the present study, we assessed patterns of collateral effects by experimentally evolving 160 independent populations of P...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535774/a-bacterial-negative-transcription-regulator-binding-on-an-inverted-repeat-in-the-promoter-for-epothilone-biosynthesis
#19
Xin-Jing Yue, Xiao-Wen Cui, Zheng Zhang, Ran Peng, Peng Zhang, Zhi-Feng Li, Yue-Zhong Li
BACKGROUND: Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified. RESULTS: We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of esi promoted the epothilone production, while overexpression of the gene suppressed the production...
May 23, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28531216/impact-of-mutations-in-toll-like-receptor-pathway-genes-on-esophageal-carcinogenesis
#20
Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O'Donovan, Nick J Gay, Rebecca C Fitzgerald
Esophageal adenocarcinoma (EAC) develops in an inflammatory microenvironment with reduced microbial diversity, but mechanisms for these influences remain poorly characterized. We hypothesized that mutations targeting the Toll-like receptor (TLR) pathway could disrupt innate immune signaling and promote a microenvironment that favors tumorigenesis. Through interrogating whole genome sequencing data from 171 EAC patients, we showed that non-synonymous mutations collectively affect the TLR pathway in 25/171 (14...
May 2017: PLoS Genetics
keyword
keyword
104574
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"